HistoBase News

Gbrowse2 disabled

Tue, 7 March 2023 12:00:00 PST

As of 3/7/2023, genome browsing has been temporarily been disabled due to a possible vulnerability in Gbrowse2, which is no longer maintained. We expect to re-introduce genome browsing later in 2023 using either jbrowse or the Sil Lab's internal genome browsing code.

HistoBase back up

Fri, 6 April 2010 11:00:00 PDT

HistoBase was unavailable from 7/23/2010 to 8/6/2010 due to a hardware failure on our webserver. As of 8/6/2010, the databases have been rebuilt on an interim webserver. We took advantage of the down time to upgrade the underlying operating system (from RHEL 4 to Debian GNU/Linux 5) and Gbrowse (from 1.65 to 2.03). Note that, due to the upgrade, javascript and cookies must be enabled in your browser in order to use most of the Gbrowse features.

All of the data and interfaces previously existing on HistoBase should now be available. We apologize for any inconvenience that the down time may have caused. Please contact Mark.Voorhies@ucsf.edu if you notice any bugs or missing data.

Updated gene links for Fg, An, Ci, and HcWU24 (Nam1)

Mon, 29 March 2010 11:00:00 PDT

Updated broken gene links for Fusarium graminearum and Aspergillus nidulans. Fusarium graminearum now links to the BROAD Fusarium multihome database. Aspergillus nidulans now links to AspGD.

Coccidioides immitis and Histoplasma capsulatum WU24 (Nam1) now link to the BROAD's comparative Dimorph Fungal Database rather than the strain-specific databases. Additionally, Michael Koehrsen has added links to HistoBase from the BROAD's WU24 gene pages.

Gbrowse download for BLAT

Sat, 20 March 2010 20:30:02 PDT

The results page for BLAT searches now has an option to download all hits in Gbrowse annotation format. Previously, the Gbrowse annotation had to be copied from the alignment details page for each hit.

Expression data

Sat, 20 March 2010 20:30:01 PDT

Expression profiles from two microarray experiments are now available on the G217B gene details pages:

PNAS 105:4880 -- relative expression of wild type and ryp1 mutant G217B at 37 or 25°C.
PLoS Pathogens 4:e10000044 -- time course expression profile for G217B in iron replete or limiting conditions.

Batch download tools

Sat, 20 March 2010 20:30:00 PDT

HistoBase now has two batch download tools:

Annotation Download -- for downloading annotations in CSV format (compatible with Excel and OpenOffice).
Sequence Download -- for downloading sequences in FASTA format.

Both tools are queried with a list of UIDs from the G217B or G186AR oligo arrays (UIDs are listed under "Oligos" in the gene details pages; e.g., G217Borfs1.21j16 for ABC1). Querying by gene name is not currently supported.

Interface updates

Tue, 18 March 2008 17:53:47 PDT

Finished several small updates to the site layout and navigation.

A top level navigation bar and quick-search box should now be present at the top of most HistoBase pages.
A Gbrowse preview image is now included in the gene detail pages.
The quick-search box now supports more general search terms (gene names, oligo names, genome loci (in Gbrowse format), and keywords).
Updated the home page.

Launch of public website

Fri, 11 May 2007 12:54:25 PDT

HistoBase, a functional annotation database for Histoplasma capsulatum, is now publicly accessible at http://histo.ucsf.edu/.

Bug fixes, data updates, and new features will be posted to this site.